AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1395380


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1395380 MtrunA17_Chr7g0273811 98.361 183 3 0 1 183 1 183 2.64e-135 375
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1395380 AT1G54500.1 62.121 198 57 7 1 183 1 195 9.04e-65 197

Find 36 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGAAAACTGTGCTTATTTA+TGG 0.158905 tig0021940:-21873 Msa1395380:CDS
GGGGTTGGTGTAATGGAGTT+TGG 0.242995 tig0021940:+22292 None:intergenic
CTTGGTGGAAATTCTCTTAC+TGG 0.257542 tig0021940:-21900 Msa1395380:CDS
AACTGAAAACCAGGTGGAAT+TGG 0.298992 tig0021940:+22032 None:intergenic
GGGTTGGTGTAATGGAGTTT+GGG 0.326512 tig0021940:+22293 None:intergenic
GGAGTTTGGGTTTGAGAGGA+TGG 0.335353 tig0021940:+22306 None:intergenic
TTGAAAAGCTTCCAGATGAT+TGG 0.347062 tig0021940:-22010 Msa1395380:CDS
TTTGCTCAGAATCAACAATA+TGG 0.354668 tig0021940:-21924 Msa1395380:CDS
AGAGGATGGATTTGAGAGAA+AGG 0.359838 tig0021940:+22320 None:intergenic
TTTGAGTTTGTTGGAGTGAT+GGG 0.360473 tig0021940:+22247 None:intergenic
ATGAAGGGGTTTGAGTTTGT+TGG 0.377386 tig0021940:+22238 None:intergenic
TTTGTTGGAGTGATGGGTTT+TGG 0.390206 tig0021940:+22253 None:intergenic
AAAGGGAGGGGTTGGTGTAA+TGG 0.410099 tig0021940:+22285 None:intergenic
AGTAAAAGTGTTGAAATTGC+TGG 0.415161 tig0021940:-21948 Msa1395380:CDS
CAGTGAAGTTTCGTGGATGA+AGG 0.418966 tig0021940:+22222 None:intergenic
GTTTGAGTTTGTTGGAGTGA+TGG 0.421219 tig0021940:+22246 None:intergenic
AGGAGTTGAGAGATGGAAAG+TGG 0.425190 tig0021940:+22340 None:intergenic
GTGGGACATCTCCAATCATC+TGG 0.448648 tig0021940:+21999 None:intergenic
GAGTTTACAGTGAAGTTTCG+TGG 0.451202 tig0021940:+22215 None:intergenic
CAGAATCAACAATATGGTCT+TGG 0.468077 tig0021940:-21918 Msa1395380:CDS
AAGTTCGCTGTGTTGAATAC+AGG 0.478954 tig0021940:-22116 Msa1395380:CDS
AATCAACAATATGGTCTTGG+TGG 0.481663 tig0021940:-21915 Msa1395380:CDS
GAGAGAAAGGAGTTGAGAGA+TGG 0.493471 tig0021940:+22333 None:intergenic
AGTGAAGTTTCGTGGATGAA+GGG 0.530603 tig0021940:+22223 None:intergenic
CCTTCGTATCCAATTCCACC+TGG 0.534697 tig0021940:-22041 Msa1395380:CDS
TAATGGAGTTTGGGTTTGAG+AGG 0.568113 tig0021940:+22302 None:intergenic
ACTTTGTGCAGCACCACAAG+TGG 0.579838 tig0021940:+21980 None:intergenic
GGTGGAAATTCTCTTACTGG+TGG 0.584178 tig0021940:-21897 Msa1395380:CDS
CCAGGTGGAATTGGATACGA+AGG 0.592505 tig0021940:+22041 None:intergenic
GTGAAGTTTCGTGGATGAAG+GGG 0.593003 tig0021940:+22224 None:intergenic
TATAAATATGATGAAGGTGT+AGG 0.596708 tig0021940:-22068 Msa1395380:CDS
TGTGGTTATAAATATGATGA+AGG 0.597525 tig0021940:-22074 Msa1395380:CDS
ATCTATGAATGTCGTTCATG+TGG 0.599864 tig0021940:-22092 Msa1395380:CDS
GATTGGAGATGTCCCACTTG+TGG 0.648504 tig0021940:-21993 Msa1395380:CDS
CTTTGTGCAGCACCACAAGT+GGG 0.685384 tig0021940:+21981 None:intergenic
CAGGTGGAATTGGATACGAA+GGG 0.702702 tig0021940:+22042 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGTGGTTATAAATATGATGA+AGG - tig0021940:22097-22116 Msa1395380:CDS 25.0%
!! TATAAATATGATGAAGGTGT+AGG - tig0021940:22103-22122 Msa1395380:CDS 25.0%
!! AGTAAAAGTGTTGAAATTGC+TGG - tig0021940:22223-22242 Msa1395380:CDS 30.0%
TTTGCTCAGAATCAACAATA+TGG - tig0021940:22247-22266 Msa1395380:CDS 30.0%
CAGAAAACTGTGCTTATTTA+TGG - tig0021940:22298-22317 Msa1395380:CDS 30.0%
!!! GGTTTTGGAAAGGAGAAAAA+GGG + tig0021940:21906-21925 None:intergenic 35.0%
!! TTTGAGTTTGTTGGAGTGAT+GGG + tig0021940:21927-21946 None:intergenic 35.0%
ATCTATGAATGTCGTTCATG+TGG - tig0021940:22079-22098 Msa1395380:CDS 35.0%
! TTTTCAAACTGAAAACCAGG+TGG + tig0021940:22148-22167 None:intergenic 35.0%
! AGCTTTTCAAACTGAAAACC+AGG + tig0021940:22151-22170 None:intergenic 35.0%
TTGAAAAGCTTCCAGATGAT+TGG - tig0021940:22161-22180 Msa1395380:CDS 35.0%
CAGAATCAACAATATGGTCT+TGG - tig0021940:22253-22272 Msa1395380:CDS 35.0%
! AATCAACAATATGGTCTTGG+TGG - tig0021940:22256-22275 Msa1395380:CDS 35.0%
!!! TTCTTTGCACTTTTTCTCAG+TGG - tig0021940:22334-22353 Msa1395380:CDS 35.0%
! AGAGGATGGATTTGAGAGAA+AGG + tig0021940:21854-21873 None:intergenic 40.0%
! TAATGGAGTTTGGGTTTGAG+AGG + tig0021940:21872-21891 None:intergenic 40.0%
TTGGAAAGGAGAAAAAGGGA+GGG + tig0021940:21902-21921 None:intergenic 40.0%
TTTGGAAAGGAGAAAAAGGG+AGG + tig0021940:21903-21922 None:intergenic 40.0%
!!! GGGTTTTGGAAAGGAGAAAA+AGG + tig0021940:21907-21926 None:intergenic 40.0%
!!! TTTGTTGGAGTGATGGGTTT+TGG + tig0021940:21921-21940 None:intergenic 40.0%
!! GTTTGAGTTTGTTGGAGTGA+TGG + tig0021940:21928-21947 None:intergenic 40.0%
! ATGAAGGGGTTTGAGTTTGT+TGG + tig0021940:21936-21955 None:intergenic 40.0%
AGTGAAGTTTCGTGGATGAA+GGG + tig0021940:21951-21970 None:intergenic 40.0%
GAGTTTACAGTGAAGTTTCG+TGG + tig0021940:21959-21978 None:intergenic 40.0%
! AAACGACGTTTTTCTGAGTC+GGG + tig0021940:22028-22047 None:intergenic 40.0%
! CAAACGACGTTTTTCTGAGT+CGG + tig0021940:22029-22048 None:intergenic 40.0%
AAGTTCGCTGTGTTGAATAC+AGG - tig0021940:22055-22074 Msa1395380:CDS 40.0%
AACTGAAAACCAGGTGGAAT+TGG + tig0021940:22142-22161 None:intergenic 40.0%
CTTGGTGGAAATTCTCTTAC+TGG - tig0021940:22271-22290 Msa1395380:CDS 40.0%
AGGAGTTGAGAGATGGAAAG+TGG + tig0021940:21834-21853 None:intergenic 45.0%
GAGAGAAAGGAGTTGAGAGA+TGG + tig0021940:21841-21860 None:intergenic 45.0%
!! GGGTTGGTGTAATGGAGTTT+GGG + tig0021940:21881-21900 None:intergenic 45.0%
TGGAAAGGAGAAAAAGGGAG+GGG + tig0021940:21901-21920 None:intergenic 45.0%
!!! TGGAGTGATGGGTTTTGGAA+AGG + tig0021940:21916-21935 None:intergenic 45.0%
GTGAAGTTTCGTGGATGAAG+GGG + tig0021940:21950-21969 None:intergenic 45.0%
CAGTGAAGTTTCGTGGATGA+AGG + tig0021940:21952-21971 None:intergenic 45.0%
CGACTCAGAAAAACGTCGTT+TGG - tig0021940:22027-22046 Msa1395380:CDS 45.0%
CAGGTGGAATTGGATACGAA+GGG + tig0021940:22132-22151 None:intergenic 45.0%
GGTGGAAATTCTCTTACTGG+TGG - tig0021940:22274-22293 Msa1395380:CDS 45.0%
! GGAGTTTGGGTTTGAGAGGA+TGG + tig0021940:21868-21887 None:intergenic 50.0%
!! GGGGTTGGTGTAATGGAGTT+TGG + tig0021940:21882-21901 None:intergenic 50.0%
!! AAAGGGAGGGGTTGGTGTAA+TGG + tig0021940:21889-21908 None:intergenic 50.0%
AAGGAGAAAAAGGGAGGGGT+TGG + tig0021940:21897-21916 None:intergenic 50.0%
CCAGGTGGAATTGGATACGA+AGG + tig0021940:22133-22152 None:intergenic 50.0%
CCTTCGTATCCAATTCCACC+TGG - tig0021940:22130-22149 Msa1395380:CDS 50.0%
GTGGGACATCTCCAATCATC+TGG + tig0021940:22175-22194 None:intergenic 50.0%
GATTGGAGATGTCCCACTTG+TGG - tig0021940:22178-22197 Msa1395380:CDS 50.0%
CTTTGTGCAGCACCACAAGT+GGG + tig0021940:22193-22212 None:intergenic 50.0%
ACTTTGTGCAGCACCACAAG+TGG + tig0021940:22194-22213 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0021940 gene 21821 22372 21821 ID=Msa1395380;Name=Msa1395380
tig0021940 mRNA 21821 22372 21821 ID=Msa1395380-mRNA-1;Parent=Msa1395380;Name=Msa1395380-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|183
tig0021940 exon 21821 22372 21821 ID=Msa1395380-mRNA-1:exon:14894;Parent=Msa1395380-mRNA-1
tig0021940 CDS 21821 22372 21821 ID=Msa1395380-mRNA-1:cds;Parent=Msa1395380-mRNA-1
Gene Sequence

>Msa1395380

ATGGCTGCTTCCACTTTCCATCTCTCAACTCCTTTCTCTCAAATCCATCCTCTCAAACCCAAACTCCATTACACCAACCCCTCCCTTTTTCTCCTTTCCAAAACCCATCACTCCAACAAACTCAAACCCCTTCATCCACGAAACTTCACTGTAAACTCTGTAGACATCTCAAATGAAGAAGATACAACTTCAGAGTCTGAAAAACCCGACTCAGAAAAACGTCGTTTGGAAGAAAAGTTCGCTGTGTTGAATACAGGAATCTATGAATGTCGTTCATGTGGTTATAAATATGATGAAGGTGTAGGTGACCCTTCGTATCCAATTCCACCTGGTTTTCAGTTTGAAAAGCTTCCAGATGATTGGAGATGTCCCACTTGTGGTGCTGCACAAAGTTTCTTTGAAAGTAAAAGTGTTGAAATTGCTGGTTTTGCTCAGAATCAACAATATGGTCTTGGTGGAAATTCTCTTACTGGTGGTCAGAAAACTGTGCTTATTTATGGTACTTTGTTGTTTTTCTTTGCACTTTTTCTCAGTGGCTACTTCATACAATAG

Protein sequence

>Msa1395380

MAASTFHLSTPFSQIHPLKPKLHYTNPSLFLLSKTHHSNKLKPLHPRNFTVNSVDISNEEDTTSESEKPDSEKRRLEEKFAVLNTGIYECRSCGYKYDEGVGDPSYPIPPGFQFEKLPDDWRCPTCGAAQSFFESKSVEIAGFAQNQQYGLGGNSLTGGQKTVLIYGTLLFFFALFLSGYFIQ*